The goal of this project is to develop proteomics technologies for the complete measurement of protein turnover in cells, focusing on the analysis of protein abundance, ubiquitination, synthetic rate, and degradation rate. According to the central dogma of molecular biology, genetic information flows from the genome to the transcriptome to the proteome. Theoretically, protein dynamics in a cellular system yields a steady state in which the level of a protein depends on its preexisting concentration, synthetic rate, and degradation rate. Protein degradation in eukaryotic cells is mainly mediated by the ubiquitin (Ub)-proteasome system and the autophagy-lysosome pathway. Ubiquitin, a small protein of 76 amino acids, modifies thousands of proteins as multifunctional signals for proteasomal degradation and other downstream events. Ubiquitin is conjugated to substrates in the form of monomers and polymers. In this application, we propose to develop novel mass spectrometry (MS)-based methods to profile protein turnover, analyze ubiquitinated proteome and ubiquitin chain structures, and study how protein turnover is affected under pathophysiological conditions. Our four specific aims are to (i) develop a 20-plex integrated MS approach for measuring proteome turnover; (ii) develop middle-down MS methods for analyzing polyubiquitin chain structures; (iii) study the function of diverse polyubiquitin chains in yeast ad mammalian cells; and (iv) investigate protein turnover alterations in mouse models of human disease. Protein turnover and ubiquitination are fundamental regulatory events, contributing to the pathogenesis of human disease. The research will lead to the development of novel MS technologies for studying protein turnover and new understanding of polyubiquitin chain function, as well as its involvement in human disease.